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OSDR MCP Server + Agents

@alwalt

Repository

Basic information

Category

Other

Transports

stdio

Author

alwalt

About OSDR MCP Server + Agents

No overview available yet

OSDR MCP Server + Agents config

Add this server to your MCP-compatible client using the configuration below.

{
  "mcpServers": {
    "osdr_mcp_server": {
      "command": "python",
      "args": [
        "first_example/main.py"
      ]
    }
  }
}

OSDR MCP Server + Agents tools

Tool list not available yet

This listing does not currently have a tool list to display. This does not mean the server has no tools; check its documentation for supported capabilities.

We auto-extract tools from the README. The maintainer can list them under a ## Tools heading to populate this section.

Overview

What is 🧠 OSDR MCP Server + Agents?

This project demonstrates how to integrate MCP agents with custom tools for interacting with NASA’s Open Science Data Repository (OSDR). It includes working examples of agent workflows that fetch, analyze, and summarize biological data using the Model Context Protocol (MCP).

How to use 🧠 OSDR MCP Server + Agents?

Clone the repository, install dependencies with pip install -r requirements.txt, then run an example (e.g., python first_example/main.py) or launch the MCP server directly (python osdr_mcp/main_simple.py). Configuration is done via cp_agent.config.yaml.

Key features of 🧠 OSDR MCP Server + Agents

  • Exposes custom MCP tools: osdr_fetch_metadata and osdr_find_by_organism
  • Includes additional RNA analysis tools in osdr_viz_tools
  • Three example agent workflows for different integration levels
  • Configurable LLM backend (Ollama, OpenAI) and MCP server connections
  • Multi-agent pipeline: fetch, quantitative analysis, and summary writing

Use cases of 🧠 OSDR MCP Server + Agents

  • Fetch metadata for a specific OSDR dataset
  • Filter OSDR studies by organism name
  • Generate a tweet-sized summary using official MCP servers
  • Download RNA count data and create a bar plot
  • Produce a markdown report summarizing biological analysis

Frequently asked questions

1

How do I configure the LLM backend?

Edit `cp_agent.config.yaml` to set the LLM backend (e.g., Ollama or OpenAI) and adjust system prompts, MCP server connections, and tool availability.

2

How do I run a specific example?

From the repo root, run `python first_example/main.py`, `python second_example/main.py`, or `python third_example/main.py` depending on the desired workflow.

3

What are the custom MCP tools available?

The `osdr_mcp` package provides `osdr_fetch_metadata` and `osdr_find_by_organism`; additional tools like RNA analysis are in `osdr_viz_tools`.

4

Where does the data come from?

All biological data is fetched from NASA’s Open Science Data Repository via its public API.

5

What are the runtime requirements?

Python and the packages listed in `requirements.txt`. Optionally, an LLM backend like Ollama or an OpenAI API key must be configured.

Comments

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